I'm just curious why close votes dont seem to count as helpful for deputy/marshal badges. It seems like they should since when you get to 3k you get your ability to flag questions replaced by vote close.
Does anyone know why this is?
Voting to close is not the same as flagging. Once you've reached 3k rep, the system trusts you enough to know when to cast a vote to close.
Flagging should be reserved for serious incidents.
If you're aiming for the badges - you can still achieve them by going through review route & use Not an Answer / Custom mod flags judiciously.
Simply, a vote to close is not a flag.
You're not flagging any more so you can't increment your helpful flag count by this method. If you are still trying to flag that something should be closed once you have passed 3K reputation then you're doing it wrong. This is why flags to close are converted to votes to close.
You can still flag for other reasons - Spam, Very Low Quality etc.
Also if you run out of close votes for the day you can revert to flagging.